HPLC-MS/MS and Metabolomics

Transcription

1 HPLC-MS/MS and Metabolomics Yu Cao Ph.D. CCIC MS&P Summer Workshop August 17, 2015 Publication in Metabolomics Number of publications per year Search engine: Web of Science Topic: metabolomics

2 Applications of metabolomics in cancer research Kathleen A. Vermeersch and Mark P. Styczynski J. Carcinogenesis, 2013, 12, doi: / Metabolomics short course at ASMS

3 INNOVATION Metabolomics: the apogee of the omics trilogy Gary J. Patti, Oscar Yanes and Gary Siuzdak Molecular Cell Biology, 2012, 13, Sample preparation 3

4 Sample Preparation Sample prep often most consuming (difficult) step Sample prep/clean-up separates interfering species from analyte Example: analysis of drug and metabolites in plasma need to remove protein interferences Off-line or in-line from MS/MS detection Sample prep/clean-up to concentrate analyte Example: Pesticides in drinking water Basic principle of sample prep involves preferential binding of analyte over interfering species or vice versa, followed by elution to MS/MS Separation technologies essential in sample prep General Considerations when dealing with samples for MS or MS/MS Ionization method? Instrument availability Sensitivity/Quantification Time of analysis In vivo sample pre-ms treatment? Chromatographic/extraction methods: the shorter, the better GC, HPLC, zip-tip, solid phase extraction (SPE), dialysis, etc. Derivatization: the simpler, the better to increase volatility (GC); to study neutral loss; to increase ionization efficiency 4

5 Types of Separation Technologies for Molecules Method Separation based on Separation done using Further steps Liquid-liquid Extraction Partitioning in one of two liquid phases Glassware Liquid-Liquid Extraction An immiscible solvent is added to the sample which then separates into 2 distinct liquid phases. Some sample analytes will go into the bottom phase (Aqueous), some will separate into the top phase (Organic) Large solvent consumption Time/labor intensive May need evaporation step >1 extraction if mixture of analytes Emulsions and contamination issues 5

6 Types of Separation Technologies for Molecules Method Separation based on Separation done using Further steps Liquid-liquid Extraction Partitioning in one of two liquid phases Glass ware Solid-phase Extraction Adsorption/ partitioning onto solid sorbent Cartridges, disks, filters, plates Solid-Phase Extraction Uses chromatographic particles Packed-bed column cartridges or similar Well established commercial technology (1978) 1000s literature refs Clean extracts Good recovery for polar analytes Sample must be in liquid state Driving force: gravity, pressure, vacuum Automation cartridges 96 well plate disk 6

7 Solid-Phase Extraction Types of Chromatography Normal Phase Non-polar mobile phase Polar stationary phase Manufacturer Brand Name Reversed Phase Most common Polar mobile phase Non-polar stationary phase Waters Varian SEP-PAK OASIS BondElute Ion Exchange Buffer/Ionic mobile phase Baker BakerBond Cationic/Anionic exchange stationary phase 3M Empore Supelco Supelclean + Many Others Solid-Phase Extraction - common protocol Procedure Sample Prepare: Homogenize, suspend, centrifuge, etc Load onto conditioned cartridge Wash off weakly retained interferences with weak solvent Elute product with strong solvent Analyze: HPLC, GC-MS, LC-MS/MS 7

8 (KNO 3 ) n K + pure analyte (control) engine oil contaminated parking lot oil same as b) after organic matter removal by SPE Gapeev, A. and Yinon, J. J. Forensic Sci. 2004, 49 Types of Separation Technologies for Molecules Method Liquid-liquid Extraction Solid-phase Extraction Separation based on Partitioning in one of two liquid phases Adsorption/ partitioning onto solid sorbent Separation done using Glass ware Cartriges, disks, filters, plates Further steps Dialysis/Ultrafiltration Molecular weight/size SlideAlyzer/tubing 8

9 Dialysis Tubing or Slide A-Lyzer Diff MWCO ranges ml capacity Useful for biologicals Sample loading here Spin filters polyethersulfone membrane (Vivaspin, ex) volumes from 100 μl to 20 ml, with a range of molecular weight cutoff values from Mr = Types of Separation Technologies for Molecules Method Liquid-liquid Extraction Solid-phase Extraction Separation based on Partitioning in one of two liquid phases Adsorption/ partitioning onto solid sorbent Separation done using Glass ware Cartriges, disks, filters, plates Further steps Dialysis/Ultrafiltration Molecular weight/size SlideAlyzer, tubing, spin filter Precipitation Solubility 9

10 HPLC Mechanism, Method Setup, Examples Retention Mechanisms Phenomenex 10

11 Retention Mechanisms Phenomenex Mobile Phase Composition Phenomenex 11

12 Phenomenex Phenomenex 12

13 Generic LC Method Development Column selection Bedding chemistry, dimension, bead size Buffers (mobile phase) Ionic strength, ph, pairing reagent Fine tune the method Temperature Gradient slope ph Selectivity Waters Corporation 13

14 ph Selectivity Waters Corporation Organic Modifier Selection Waters Corporation 14

15 Chart of Mobile Phase Selection Waters Corporation Column Type Column Configurations and Applications ID (mm) Length (mm) Particle Size (m) Flow Rate Ranges Applications Sensitivity Increase Nano nl/min Capillary 0.3, , L/min Micro Bore , L/min Narrow Bore , ml/min Analytical , ml/min Semi-prep ml/min Preparative , ml/min Proteomics, Sample Limited PTM Characterization Peptide Mapping LC/MS High Sensitivity LC/MS Sample Limited. LC/MS Analytica; 1 Small Scale protein purification CombiChem purification

16 Column Comparison by Vendors Imtakt Phenomenex Waters Others Details refer to the pdf files en.pdf LC Tips on Peak Shape Issues 16

17 LC Tips on Peak Shape Issues LC Tips on Peak Shape Issues 17

18 Metabolomics in MS&P Projects going on Sample type: Eerie lake project Amino acid analysis in animal models Oligonucleotide project Unknown identification in smoker plasma Honey bee project Drug stability TMAO analysis for breast cancer study Plant extract Coating material Environmental Bio-fluid Tissues etc. Mass spec analysis Untargeted metabolomics: Q-TOF Targeted metabolomics: Q-TOF and QQQ 18

19 Q-TOF Q1 q2 TOF Benefits: Higher resolution & mass accuracy All ions recorded in parallel Ref: Chemushevich, 2001 Chromatogram of Oligonucleotides std on Q-TOF Intens. x Time [min] Olistd_040815_03_BE4_01_171.d: BPC -All MS Sample: Bruker standard and (MW: 1K~10K Da) 19

20 MS of Peak 1 at 2.4 min Intens. x MS, 2.4min # x x m/z MS, 2.4min # m/z MS, 2.4min # m/z MS of Peak 6 at 19.0 min Intens. x MS, 19.0min # x m/z MS, 19.0min # m/z MS, 19.0min # m/z 20

21 Untargeted metabolomics RPLC-MS Intens. x MS - L_6996_062014_01_BB5_01_1132.d: BPC -All MS 2 Intens. 0 x MS + L_6996_061914_01_BB5_01_1108.d: BPC +All MS Time [min] RPLC-MS at 32.7 min Intens. x L_6996_062014_01_BB5_01_1132.d: MS, 32.7min #1963 MS Intens. x L_6996_061914_01_BB5_01_1108.d: MS, min #1965 m/z MS m/z 21

22 Untargeted HILIC-LC-MS Intens. x MS - L_6996_062214_01_BB5_01_1181.d: BPC -All MS 2 Intens. 0 x MS + L_6996_062314_01_BB5_01_1206.d: BPC +All MS Time [min] HILIC-MS at 18.2 min Intens. x L_6996_062214_01_BB5_01_1181.d: MS, 18.2min #1092 MS Intens. x L_6996_062314_01_BB5_01_1206.d: MS, min #1093 m/z MS m/z 22

23 Chromatogram of m/z at RPLC v.s. HILIC Intens. x10 4 L_6996_061914_01_BB5_01_1108.d: EIC ±0.1 +All MS Intens. 0.0 x10 5 L_6996_062314_01_BB5_01_1206.d: EIC ±0.1 +All MS Time [min] Targeted metabolomics Cl N HN N N 100 % 256.0/209.0 Imi;6.24; ; e+006 O - N + O N Cl N N + O O - Imidacloprid NH N H Clothianidin HN N D D N N + O O - S N D D Cl Imidacloprid-d4 (Int. Std.) _30349_STD_GS_IS L_50 sample after GS, centrifuge, filter, fresh prep in 50%B 100 % _30349_STD_GS_IS L_50 sample after GS, centrifuge, filter, fresh prep in 50%B 100 % / /213.0 Clo;6.14; ; IS;6.25; ; min F1:MRM of 1 channel,es+ TIC 3.462e+006 min F3:MRM of 1 channel,es+ TIC 2.174e+007 What are we detecting and which instrument is used??? min 23

24 QQQ Q3 Q1 q2 Benefits: Simple, ion filter Good for quantification MS/MS Scan Modes Product Ion Scan Select Dissociate Scan Precursor Ion Scan Scan Dissociate Select Neutral Loss Scan Scan Dissociate Scan Selected Reaction Monitoring (SRM) Select Dissociate Select 24

25 Selected Reaction Monitoring Source Q1 (gas) Q3 Detector Select one m/z (fixed V ac /V dc ) MS/MS at different collision energies Thermo provided data base 25

26 Quantitation upon AUC Compound name: Clo Correlation coefficient: r = , r^2 = Calibration curve: * x Response type: Internal Std ( Ref 4 ), Area * ( IS Conc. / IS Area ) Curve type: Linear, Origin: Include, Weighting: 1/x, Axis trans: None Std curve QCs Samples Blanks Compound name: Imi Correlation coefficient: r = , r^2 = Calibration curve: * x Response type: Internal Std ( Ref 4 ), Area * ( IS Conc. / IS Area ) Curve type: Linear, Origin: Include, Weighting: 1/x, Axis trans: None Response Response ng/ml ng/ml Bioinformatics in Metabolomics 26

27 ESI-MS n Libraries # Spectra # Compounds Notes METLIN > 68,000 13,048 Public, no download mzcloud > 416,000 2,975 Public, no download MoNA > 236,000 69,946 Public, no download MassBank > 28,100 > 43,000 Public, downloadable HMDB 9,500 Public, downloadable GNPS > 9,000 ~2200 NP Public, downloadable ReSpect (MS n ) > 9,000 3,595 Public, downloadable NIST14 MS/MS > 234,000 9,344 Commercial Wiley MSforID > 10,000 > 1,200 Commercial MetabolomicsWorkBench Public, no download LipidBlast 200,000 Public, downloadable Lipid Maps 37,500 Public, downloadable LipidSearch >1500,000 lipid ions Commercial Database search Progenesis QI 27

28 Import data Data alignment MS + MS - 28

29 Peak picking MS + MS - Review deconvolution 29

30 Identify compounds Review compounds 30

31 Pathway analysis Other Computational Tools for Metabolomics MS-DIAL Data dependent and/or independent MS/MS experiments MS-FINDER GC/MS data alignment, database search (commercial) 31

32 Anal. Chem. 2014, 86, Anal. Chem. 2014, 86,

33 Thank you! 33